1. Field of the Invention
The present invention relates to the art of designing oligonucleotide probes suitable for a nucleic acid sequence analysis system using so-called DNA microarrays or the like.
2. Description of the Related Art
There conventionally have been known systems for gene manifestation and sequence determining systems using DNA microarrays, as described in Japanese Patent Laid-Open No. 10-272000 and Japanese Patent Laid-Open No. 11-1187900. With the system disclosed in these Patent Documents, there is the need to design probes for hybridizing with specimens beforehand, unlike DNA microarrays created through spots with cDNA. In the event that a suitable probe can be designed well, information regarding base sequence fragments in a specimen can be obtained at an extremely high probability.
With this system, it is unusual for even the longest base sequences used as probes to reach 100 or more in length, and short base sequences are just a few bases in length. That is to say, with the system disclosed in these Patent Documents, a particular base sequence is trapped using a probe of a base sequence which is far shorter than cDNA. Accordingly, there is the need for the uniqueness of a portion of the base sequence used as the probe in the DNA to be extremely high.
With the conventional selection method for selecting a portion with a high level of uniqueness described above, uniqueness evaluation is performed with regard to general sequences. For example, in the event of creating a DNA microarray for DNA from a human genome, uniqueness was checked for all human genome base sequences, and a portion with a high level of uniqueness was selected as a probe base sequence.
However, there has been a problem with the conventional selecting method in that, in the event that extremely similar base sequences are contained in a specimen, and the similar base sequences include base sequences belonging to one group and base sequences belonging to another group, determining whether each base sequence belongs to that group is extremely difficult. More specifically, at the time of making a determination for an infection or the like, there has been the problem that it is extremely difficult to find a probe which exhibits the same degree of hybrid strength regarding a DNA base sequence of the same strain of bacteria and which exhibits a different degree of hybrid strength regarding a DNA base sequence of another strain of bacteria.
Also, with the conventional method, in the event of searching for locations unique to an organism or common locations in polymorphic loci in extremely similar base sequences, all of the polymorphic base sequences are displayed for the subject organism using multiple alignment or the like, and human workers view these and select appropriate portions. This conventional method allows human error, and also results in difference in results from one worker to another.